Tuesday, August 30, 2011

To The Flint Last Sunday

I think 10 of us made it to the Flint on Sunday to run a trifecta: driftnetting, transects for darter habitat niche, and collecting silver shiners and blotched chubs. It was a beautiful day with low water, and we finished everything in just over 4 hours. One thing I've learned about silver shiners is that they travel in tight schools; if you catch one, you'll probably catch nine. We ended with 28 of them, including 3 subadults, and about 30 chubs. We plan to check both gonadal condition, and the status of gill parasites.

I'm now up to 40 DNA extractions on the Telogia project. Once I get the sequences all I have to do is analyze the data... it will be interesting one way or another.

Robert and Kara spent time with the confocal microscope trying to get informative images of gill parasites. My colleague Lynn was very impressed with what she saw of the images, but Robert didn't seem as happy; I still have to see them myself.

Tuesday, August 23, 2011

Yeah, More DNA!

My big accomplishment of the week to date is 6 DNA extractions yesterday, and 6 more today, so that I've done 28 now that are ready to be sequenced. Thursday I might get crazy and try to do another 12, the maximum I can do at once because I'm limited by the number of tube slots in the tabletop centrifuge. It's like real biology!

We're also starting to organize for a life history study of both silver shiners and blotched chubs from the Flint. Four students are interested in working on this project (one of them a volunteer), so hopefully this will fly. I'll have a better idea after Sunday's trip to the Flint.

Sunday, August 21, 2011

With The New School Year...

With the new school year I'm definitely off and running. I have three students who are willing and hopefully able to work on examining both silver shiner and blotchside chub populations in the Flint River, the basic stuff like length, sex, and reproductive condition. I also hope that we can establish how widespread the silver shiners in particular are in the river. Another student has volunteered to look at gill parasites in the silvers; I talked to Don Cloutman from Bemidji State the other day and he told he that he has described Dactylogyrus gill parasites from more than 200 North American cyprinids including the silver shiner, and with that he's about ready to retire apparently.

Others are working on the driftnet project (two more months to go) and on the Brachyrhaphis I collected in Panama. So it could be good for raw data generated.

And meanwhile Brian and Robert are close to finished with their field work on darters and will hopefully defend in the spring.

We plan on doing a big day on the Flint next Sunday, with driftnetting, transecting and netting for silver shiners and blotchside chubs. As long as we can park in a secure, convenient place it should be almost easy....

Monday, August 15, 2011

I've Been A Boring DNA Extractor

I now have a total of 16 DNA extractions related to the Telogia project. Six of them were done today. It requires a 3-hour water bath incubation at 55 deg. C at the beginning to give the protease opportunity to break down the cells and especially the nucleus. Since school begins Wednesday, I was able to use these three hours to talk to a bunch of different people about courses, teaching intro biology labs, and general business before I had to duck out and get back in the lab for the last stages of the process that involve cleaning and concentrating the DNA product. If I have a whole day open I will try to do 12 at once, my limitation since our countertop ultracentrifuge only has a capacity for 12 tubes, and much of this process involves short centrifuging bursts. After three rounds with this extraction kit I think I almost know what I'm doing, and I haven't dropped or blown up any tubes.

One and maybe two students are seriously interested in working on a project to describe the life histories of the silver shiner and blotchside chub in the Flint River. My plan is to take 20 roughly monthly, and monitor size classes, sex ratio, and gonadal development in the spring. The trick to this will be what we can do over the winter when the river is higher and faster (besides be careful!). There's some literature on the silver shiner's life history at the extreme northern edges of its range in Michigan and southern Ontario. One broad question we will try to address is how different is the species' life history here at the extreme southern edge of its range. It could be fun!

Tuesday, August 09, 2011

Now I Have 4 cyt-b Sequences, And On To A Silver Shiner Project

I now have four entire cyt-b DNA sequences, from Fundulus heteroclitus from Warwick, RI, and Oyster Pond (Cape Cod), MA, and from an F. similis from St. Joe Beach, FL, and an F. diaphanous from Warwick, RI. The latter is markedly different from the others, not surprising since the species is more distantly related to the others.

We hope to begin a population study of silver shiners, Notropis photogenis, from the Flint River. The hope is to document size and age classes, and also reproductive effort measures such as GSI. I think the species has been best studied at the far northern edge of its range in Michigan and Ontario, so we'll attempt some of the same studies here at the far southern edge of the range. By coincidence, I met a student yesterday who told me of a fairly easy river access point on Ryland Pike about a mile downstream of where we've been working, that could be useful information.

Tuesday, August 02, 2011

Another Sequence, And I've Finally Begun The Telogia Fish

I stitched together a second cytochrome-b gene last night, all 1140 bases, from a mummichog from Oyster Pond in Falmouth, MA, on the Cape. It differs by only one base from a mummichog from Maine whose sequence I have. I also have sequence data from a mummichog from Rhode Island that I'll do next, I'm curious to see if it's more different from the Maine fish.

And I finally started today for real on setting up the fish from the Telogia collection for sequencing. I'm pulling out a few fish from each of the 10 locations we have, measuring them, giving them a name like TCR1, and each fish gets its own screw-cap test tube with 95% ethanol until I cut off a small piece for DNA. We'll see how the cyt-b sequences turn out on these fish, hopefully sooner than later.